HDA3_YEAST
ID HDA3_YEAST Reviewed; 655 AA.
AC Q06623; D6W4H9;
DT 25-OCT-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 155.
DE RecName: Full=HDA1 complex subunit 3;
DE AltName: Full=Histone deacetylase complex 1 subunit 3;
GN Name=HDA3; Synonyms=PLO1; OrderedLocusNames=YPR179C;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169875;
RA Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W.,
RA Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D.,
RA Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E.,
RA Churcher C.M., Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H.,
RA DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N.,
RA Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K.,
RA Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M.,
RA Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A.,
RA Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S.,
RA Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D.,
RA Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S.,
RA Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B.,
RA Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A.,
RA Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R.,
RA Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A.,
RA Vo D.H., Hani J.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI.";
RL Nature 387:103-105(1997).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [3]
RP FUNCTION, AND IDENTIFICATION IN THE HDA1 HISTONE DEACETYLASE COMPLEX.
RX PubMed=8663039; DOI=10.1074/jbc.271.26.15837;
RA Carmen A.A., Rundlett S.E., Grunstein M.;
RT "HDA1 and HDA3 are components of a yeast histone deacetylase (HDA)
RT complex.";
RL J. Biol. Chem. 271:15837-15844(1996).
RN [4]
RP FUNCTION, AND INTERACTION WITH HDA1 AND HDA3.
RX PubMed=11287668; DOI=10.1073/pnas.081560698;
RA Wu J., Carmen A.A., Kobayashi R., Suka N., Grunstein M.;
RT "HDA2 and HDA3 are related proteins that interact with and are essential
RT for the activity of the yeast histone deacetylase HDA1.";
RL Proc. Natl. Acad. Sci. U.S.A. 98:4391-4396(2001).
RN [5]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [6]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
CC -!- FUNCTION: Required for activity of HDA1 histone deacetylase complex.
CC The HDA1 histone deacetylase complex is responsible for the
CC deacetylation of lysine residues on the N-terminal part of the core
CC histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for
CC epigenetic repression and plays an important role in transcriptional
CC regulation, cell cycle progression and developmental events.
CC {ECO:0000269|PubMed:11287668, ECO:0000269|PubMed:8663039}.
CC -!- SUBUNIT: Heterodimer with HDA2. Component of the HDA1 histone
CC deacetylase complex composed of at least one HDA1 homodimer and one
CC HDA2/HDA3 heterodimer. Interacts with HDA1 and HDA3.
CC {ECO:0000269|PubMed:11287668, ECO:0000269|PubMed:8663039}.
CC -!- INTERACTION:
CC Q06623; P53973: HDA1; NbExp=6; IntAct=EBI-38663, EBI-8206;
CC Q06623; Q06629: HDA2; NbExp=5; IntAct=EBI-38663, EBI-32800;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:14562095}.
CC -!- MISCELLANEOUS: Present with 1100 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the HDA2/3 family. HDA3 subfamily.
CC {ECO:0000305}.
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DR EMBL; U25842; AAB68112.1; -; Genomic_DNA.
DR EMBL; BK006949; DAA11595.1; -; Genomic_DNA.
DR PIR; S59836; S59836.
DR RefSeq; NP_015505.1; NM_001184276.1.
DR PDB; 3HGQ; X-ray; 3.00 A; A/B/C/D=6-333.
DR PDB; 3HGT; X-ray; 2.20 A; A/B=6-333.
DR PDB; 6Z6F; EM; 3.11 A; D=28-639.
DR PDB; 6Z6H; EM; 8.55 A; D/J=28-639.
DR PDB; 6Z6O; EM; 3.80 A; D/H/L/P=28-639.
DR PDB; 6Z6P; EM; 4.43 A; M=28-639.
DR PDBsum; 3HGQ; -.
DR PDBsum; 3HGT; -.
DR PDBsum; 6Z6F; -.
DR PDBsum; 6Z6H; -.
DR PDBsum; 6Z6O; -.
DR PDBsum; 6Z6P; -.
DR AlphaFoldDB; Q06623; -.
DR SMR; Q06623; -.
DR BioGRID; 36351; 416.
DR ComplexPortal; CPX-1884; HDA1 histone deacetylase complex.
DR DIP; DIP-4636N; -.
DR IntAct; Q06623; 7.
DR MINT; Q06623; -.
DR STRING; 4932.YPR179C; -.
DR iPTMnet; Q06623; -.
DR MaxQB; Q06623; -.
DR PaxDb; Q06623; -.
DR PRIDE; Q06623; -.
DR EnsemblFungi; YPR179C_mRNA; YPR179C; YPR179C.
DR GeneID; 856309; -.
DR KEGG; sce:YPR179C; -.
DR SGD; S000006383; HDA3.
DR VEuPathDB; FungiDB:YPR179C; -.
DR eggNOG; ENOG502QT9V; Eukaryota.
DR HOGENOM; CLU_026579_0_0_1; -.
DR InParanoid; Q06623; -.
DR OMA; NTSGDYW; -.
DR BioCyc; YEAST:G3O-34304-MON; -.
DR EvolutionaryTrace; Q06623; -.
DR PRO; PR:Q06623; -.
DR Proteomes; UP000002311; Chromosome XVI.
DR RNAct; Q06623; protein.
DR GO; GO:0005829; C:cytosol; IDA:SGD.
DR GO; GO:0070823; C:HDA1 complex; IDA:SGD.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0003682; F:chromatin binding; IDA:SGD.
DR GO; GO:0003677; F:DNA binding; IDA:SGD.
DR GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR GO; GO:0007059; P:chromosome segregation; IMP:SGD.
DR GO; GO:0031047; P:gene silencing by RNA; IMP:SGD.
DR GO; GO:0016575; P:histone deacetylation; IDA:SGD.
DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IDA:ComplexPortal.
DR Gene3D; 3.40.50.12360; -; 1.
DR InterPro; IPR038609; HDA1_su2/3_sf.
DR InterPro; IPR021006; Hda2/3.
DR InterPro; IPR026216; HDA3.
DR Pfam; PF11496; HDA2-3; 1.
DR PRINTS; PR02093; HDA1SUBUNIT3.
PE 1: Evidence at protein level;
KW 3D-structure; Chromatin regulator; Coiled coil; Nucleus;
KW Reference proteome; Repressor; Transcription; Transcription regulation.
FT CHAIN 1..655
FT /note="HDA1 complex subunit 3"
FT /id="PRO_0000083932"
FT REGION 635..655
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 482..632
FT /evidence="ECO:0000255"
FT COMPBIAS 641..655
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT STRAND 29..35
FT /evidence="ECO:0007829|PDB:3HGT"
FT HELIX 39..51
FT /evidence="ECO:0007829|PDB:3HGT"
FT HELIX 53..61
FT /evidence="ECO:0007829|PDB:3HGT"
FT TURN 62..65
FT /evidence="ECO:0007829|PDB:3HGT"
FT HELIX 68..86
FT /evidence="ECO:0007829|PDB:3HGT"
FT HELIX 88..90
FT /evidence="ECO:0007829|PDB:3HGT"
FT HELIX 93..95
FT /evidence="ECO:0007829|PDB:6Z6F"
FT HELIX 105..111
FT /evidence="ECO:0007829|PDB:3HGT"
FT HELIX 114..126
FT /evidence="ECO:0007829|PDB:3HGT"
FT STRAND 131..137
FT /evidence="ECO:0007829|PDB:3HGT"
FT HELIX 141..150
FT /evidence="ECO:0007829|PDB:3HGT"
FT HELIX 151..153
FT /evidence="ECO:0007829|PDB:6Z6F"
FT STRAND 156..162
FT /evidence="ECO:0007829|PDB:3HGT"
FT STRAND 175..184
FT /evidence="ECO:0007829|PDB:3HGT"
FT TURN 188..190
FT /evidence="ECO:0007829|PDB:3HGT"
FT STRAND 200..204
FT /evidence="ECO:0007829|PDB:3HGT"
FT HELIX 214..220
FT /evidence="ECO:0007829|PDB:3HGT"
FT STRAND 235..240
FT /evidence="ECO:0007829|PDB:3HGT"
FT HELIX 244..254
FT /evidence="ECO:0007829|PDB:3HGT"
FT HELIX 260..272
FT /evidence="ECO:0007829|PDB:3HGT"
FT HELIX 273..275
FT /evidence="ECO:0007829|PDB:3HGT"
FT TURN 282..284
FT /evidence="ECO:0007829|PDB:3HGT"
FT HELIX 285..289
FT /evidence="ECO:0007829|PDB:3HGT"
FT TURN 290..292
FT /evidence="ECO:0007829|PDB:3HGT"
FT HELIX 293..295
FT /evidence="ECO:0007829|PDB:3HGT"
FT HELIX 296..300
FT /evidence="ECO:0007829|PDB:3HGT"
FT HELIX 319..327
FT /evidence="ECO:0007829|PDB:3HGT"
FT HELIX 405..442
FT /evidence="ECO:0007829|PDB:6Z6F"
FT STRAND 446..448
FT /evidence="ECO:0007829|PDB:6Z6F"
FT HELIX 449..514
FT /evidence="ECO:0007829|PDB:6Z6F"
FT STRAND 517..520
FT /evidence="ECO:0007829|PDB:6Z6F"
FT HELIX 523..632
FT /evidence="ECO:0007829|PDB:6Z6F"
FT HELIX 634..638
FT /evidence="ECO:0007829|PDB:6Z6F"
SQ SEQUENCE 655 AA; 75463 MW; CC8F8F73D6B78E45 CRC64;
MDLLRILDTK PIPTIVDATT LGISGNTSGD YWLPTTMSLY QKELTDQIVS LHYSDILRYF
ETSHYKEDVI LESMKTMCLN GSLVATHPYL LIDHYMPKSL ITRDVPAHLA ENSGKFSVLR
DLINLVQEYE TETAIVCRPG RTMDLLEALL LGNKVHIKRY DGHSIKSKQK ANDFSCTVHL
FSSEGINFTK YPIKSKARFD MLICLDTTVD TSQKDIQYLL QYKRERKGLE RYAPIVRLVA
INSIDHCRLF FGKKFDKNSR EYLENVTAAM VILRDRLGTL PPDLRPIYSQ KLHYLVEWLE
NPTVPWPLPD IYPLKQYTSM DVERSLLTEV HFKKSDDQLE DAFSNCSKKR GRHGANKAAS
STVAGIEDNI TPSFYSTKRL KNDYYTNPLK QDMTQLTGIT TADNSSNVNY HLSSGIITHK
LIQSMGEVYM DICVQKQELD DYSCLDDLQN DHLKFFSNED EKIIKEYETV LRTNNENLNR
SHELEVENNL KFSQIETLEK DIETLKGSLM AQGETLSKLK DAFVKTDNVQ DEIEKEERVS
VSRDTEKKYM EQEIKRAVDA IRENEEETHK LNEKQNGLES ELKLKFEKSE ISTKELNEKI
GFLKKELKLE NDLNEELVGQ LSKTMDNLEN LTIPRVRTQN GNTKKKSRAK KPGNV
